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                                                                    Exhibit 10.1


                                 April 29, 2001

Vertex Pharmaceuticals Incorporated
130 Waverly Street
Cambridge, MA 02139

Re:      Stockholder Agreement

Gentlemen:

         The undersigned (the "Stockholder") owns of record and beneficially the
number of shares (the "Shares") of common stock of Aurora Biosciences
Corporation, a Delaware corporation ("Target"), as set forth below. It is
contemplated that Target, Vertex Pharmaceuticals Incorporated, a Massachusetts
corporation ("Acquiror") and Ahab Acquisition Sub, Inc., a Delaware corporation
and a newly organized wholly owned subsidiary of Acquiror ("Merger Sub"), will
enter into an Agreement and Plan of Merger (the "Agreement") with respect to the
merger (the "Merger") of Merger Sub with and into Target. Pursuant to the
Merger, each outstanding share of Target common stock will be converted into the
right to receive shares of Acquiror's common stock, all as more specifically
provided in the Agreement. The Stockholder wishes to facilitate the proposed
Merger and acknowledges that the proposed Merger will benefit the Stockholder.

         In consideration of the foregoing, and for other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, and
intending to be legally bound hereby, the Stockholder agrees as follows:

         1.       STANDSTILL. Except in connection with the Merger, the
Stockholder agrees that, until the earlier of the Effective Time (as defined in
the Agreement), or the termination of the Agreement in accordance with its
terms, Stockholder shall not offer, sell, contract to sell, transfer or
otherwise dispose of, or grant any option to purchase, or convert, any of the
Shares. The restrictions on transfer contained in this Paragraph 1 shall not
apply to transfers by the Stockholder (i) to the Stockholder's spouse, children
or other member of the Stockholder's immediate family, or a trust for the
benefit of such persons, (ii) to the trustee or trustees of a trust revocable
solely by the Stockholder, (iii) to the Stockholder's guardian or conservator,
or (iv) in the event of the Stockholder's death, to the Stockholder's
executor(s), administrator(s) or trustee(s) under the Stockholder's will
(collectively, the "Permitted Transferees"); provided, however, that in any such
event the Shares so transferred in the hands of each such Permitted Transferee
shall remain subject to the provisions of this Agreement, and each such
Permitted Transferee shall so acknowledge in writing as a condition precedent to
the effectiveness of such transfer. As security for the Stockholder's
obligations under this paragraph, the Stockholder hereby assigns to and grants
to Acquiror a lien upon and a security interest in the Shares.

         2.       PROXY.

         (a)      As further security for the Stockholder's obligations under
paragraph 1, the Stockholder hereby (i) revokes any previous proxies relating to
the Shares and (ii) irrevocably appoints, Joshua Boger, Chairman and Chief
Executive Officer of Acquiror, Vicki Sato, President of Acquiror, and Sarah
Cecil, Corporate Counsel of the Acquiror, and each of them, attorneys and
proxies, with power of substitution in each of them, of the Stockholder to (w)
attend any and all meetings (and at all adjournments, continuations or
postponements, thereof) (the "Meeting(s)") of the stockholders of Target at
which the Merger is presented for approval of such stockholders, (x) represent
the Stockholder at any such Meeting(s), (y) vote the Shares in favor of the
Merger on the terms set forth in the Agreement as executed (with such changes as
are not material to the rights of the Stockholder in the Merger) at any such
Meeting(s) and to vote the Shares in favor of other matters in connection
therewith, and (z) otherwise act for the Stockholder in the same manner and with
the same effect as if the Stockholder were personally present at such Meeting(s)
and voting the Shares or personally acting on any matters in connection with the
Merger submitted to the stockholders of Target for approval or consent
(including executing waivers and consents in connection with the Merger). Joshua
Boger, Vicki Sato and Sarah Cecil hereby agree that they shall vote the Shares
at any such Meeting(s) in favor of the Merger on the terms set forth in the
Agreement as executed (with such changes as are not material to the rights of
the Stockholder in the Merger), and with respect to other matters in connection
therewith, provided, however, that the Acquiror's conditions to closing set
forth in the Agreement have been satisfied.

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         (b)      The Stockholder authorizes such proxies to substitute any
other person or persons to act hereunder, to revoke any such substitution and to
file this proxy and any such substitution or revocation with the Secretary of
Target.

         (c)      THIS PROXY IS IRREVOCABLE AND COUPLED WITH AN INTEREST AND
SHALL TERMINATE ON THE EARLIER OF THE EFFECTIVE TIME OR THE TERMINATION OF THE
AGREEMENT PURSUANT TO THE TERMS THEREOF.

         3.       REPRESENTATIONS AND WARRANTIES BY STOCKHOLDER. The Stockholder
represents and warrants to Acquiror that:

         (a)      the Stockholder has all necessary power and authority to
execute this letter agreement including the proxy appointment contained herein;

         (b)      this letter agreement and proxy has been duly executed and
delivered by the Stockholder and constitutes a valid and binding agreement of
the Stockholder, enforceable in accordance with its terms; and

         (c)      neither the execution nor delivery of this letter agreement
and proxy by the Stockholder will (i) require the consent, waiver, approval,
license or authorization, or any filing with, any person or public authority,
(ii) with or without the giving of notice or the lapse of time, or both,
conflict with or constitute a violation of, or default under, or give rise to
any right of acceleration under any indenture, contract, commitment, agreement,
arrangement or other instrument of any kind to which the Stockholder is a party
or by which the Stockholder is bound, or (iii) violate any applicable law, rule,
regulation, judgment, order or degree of any governmental instrumentality or
court having jurisdiction over the Stockholder.

         4.       MISCELLANEOUS.

         (a)      The Stockholder will not take any action that would prevent or
frustrate Acquiror's rights under the Agreement.

         (b)      The Stockholder acknowledges receipt of the Acquiror's Annual
Report on Form 10-K for the year ended December 31, 2000.



           [The remainder of this page is intentionally left blank.]

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         IN WITNESS WHEREOF, the Stockholder has executed this agreement and
proxy as of the date and year first above written.

                                    STOCKHOLDER:

                                    (Individual)

                                    /s/ Stuart J.M. Collinson
                                    --------------------------------------------
                                    Print Name: Stuart J.M. Collinson Ph.D.
                                                --------------------------------


                                    (Entity)


                                    --------------------------------------------
                                    By:
                                       -----------------------------------------
                                       Name:
                                            ------------------------------------
                                       Title:
                                             -----------------------------------

                                    Number of Shares of
                                    Common Stock    3,453
                                                --------------------------------


The undersigned hereby acknowledges their obligation to vote the Shares at any
Meeting(s) in favor of the Merger as provided in Section 2(a) hereof.


/s/ Joshua Boger
------------------------------
Joshua Boger

/s/ Vicki Sato
------------------------------
Vicki Sato

/s/ Sarah Cecil
------------------------------
Sarah Cecil

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                     Schedule of Other Stockholders Signing
                       This Form of Stockholder Agreement


Timothy J. Wollaeger
Wendell Wierenga
Roy A. Whitfield
Harry Stylli
Hugh Y. Rienhoff, Jr.
John Pashkowsky
Paul A. Negulescu
John D. Mendlein
Christopher W. Krueger
Thomas G. Klopack
Ralph Kauten
The Kauten Family LLC
James C. Blair